The two stacks can then be merged via: Image › Color › RGB merge. You can also choose to check a box for whether or not the source stacks should be kept. This can be done with Image › Stacks › Tools › Deinterleave and entering the number of channels in the dialog (typically “2”). The stack needs to be “De-interleaved” before it can be RGB-merged. Slice 1 is Timepoint1-channel1 and Slice 2 is Timepoint1-channel2. Multi-channel experiments acquired on some systems are imported with the different channels interleaved, i.e. Merging multi-channel images Interleaved multi-channel experiments To convert it back to a composite you can use the menu command Image › Color › Make Composite. Sometime the composite can revert to a multi-slice stack. The disadvantage of the Composite image type is that this relatively recent Fiji development is not supported by all existing plugins.
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